Approximate dependence of sequence alignment accuracy and expected models accuracy on the percentage of sequence identity. The classification of model accuracy (see Table 1) practically agrees with alignment accuracy, which falls into one of the following three zones of sequence similarity (defined by Rost15): safe, twilight, and midnight zone. The twilight zone denotes a huge drop in alignment accuracy (roughly in the range of 25%–30% of sequence identity) from the safe zone (high level of sequence similarity—proteins also have similar structures and functions) to the midnight zone (low level of sequence similarity—protein similarity cannot be detected from sequence comparisons alone).

Results of TR592 refinement from the CASP9 refinement competition. Top: Three superimposed structures are shown—native in blue, starting model in gray [coordinate root mean square deviation (crmsd): 1.26], and the best model in magenta (crmsd: 0.96). Significant improvement from the starting model can be observed in the loop region marked with a circle. It is noteworthy that this region was pointed out by the competition assessors to the participating groups as one of the main areas for refinement. Bottom: In the same size and orientation as mentioned above; all the predicted models (designated by participating groups as the best) are shown in magenta, together with the native in blue (a few heavily mismatched models were removed for clarity).

Distribution of Δcrmsd (coordinate root mean square deviation) for each method. Successful results are below the red dashed line. Only for eight of 34 methods have the sets of the resulting structures mean Δcrmsd lower than zero.

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The official website of 9th Community Wide Experiment on the Critical Assessment of Techniques for Protein Structure Prediction. Available at: http://predictioncenter.org/casp9/. (Accessed August 3, 2011).